2VD1

Complex structure of prostaglandin D2 synthase at 2.25A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PD2PDB ENTRY 1PD2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.4PEG 6000 30%, TCEP 5MM, GSH 5MM, DIOXANE 1%, MGCL2 5MM, TRISHCL (PH8.4) 50 MM
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.521α = 90
b = 123.521β = 90
c = 106.289γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2004-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.258798.50.126.63.4372851.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3197.50.521.73.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PD22.255034207181195.10.1880.1840.255RANDOM25.05
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.480.48-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.454
r_dihedral_angle_4_deg13.949
r_dihedral_angle_3_deg12.536
r_dihedral_angle_1_deg2.995
r_scangle_it2.422
r_scbond_it1.6
r_angle_refined_deg1.467
r_mcangle_it1.246
r_mcbond_it0.745
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.454
r_dihedral_angle_4_deg13.949
r_dihedral_angle_3_deg12.536
r_dihedral_angle_1_deg2.995
r_scangle_it2.422
r_scbond_it1.6
r_angle_refined_deg1.467
r_mcangle_it1.246
r_mcbond_it0.745
r_nbtor_refined0.31
r_nbd_refined0.206
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.17
r_symmetry_hbond_refined0.132
r_chiral_restr0.109
r_metal_ion_refined0.098
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6418
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing